FIGURE LEGEND
FIGURE 1 The two-level SVM prediction system.
FIGURE 2 The protein structure of PI3K and p85 \(\mathbf{\alpha}\) complex . The PI3K and p85\(\alpha\)complex (PDB ID: 5DXU) is drawn in the cartoon by PyMOL (Schrödinger, 2015). PI3K is colored wheat, and the p85a is colored in gray. The ARG104 presented in green spheres is a neutral SAV when mutated to CYS. The other residues presented in pink spheres are all cancer-related SAVs.
FIGURE 3 The superimposed of the structure of CD23 apo form and holo form from the complex of CD23 bound to Ca2+ and Fc \(\mathbf{\varepsilon}\)3-4. The structure of the Ca2+ free wild type CD23 lentic domain (PDB ID:4G96) (Yuan et al., 2013) is represented in the green cartoon. The structure of CD23 holo form bound to Ca2+ complexed with Fc\(\varepsilon\)3-4 (PDB ID: 4GKO) (Yuan et al., 2013) is drawn in gray and wheat cartoons. Ca2+ is shown in a yellow bubble, and a close-up view shows the interface of CD23 and Fc\(\varepsilon\)3-4. The D227 of the CD23 apo form is shown in the green stick. The salt-bridges forming residues in the CD23 holo form and Fc\(\varepsilon\)3-4 complex, are also highlighted with sticks.
FIGURE 4 The boxplot of the micro-environment descriptors in the ASP altered to the TYR sub-group. All micro-environment descriptors are divided in nine groups, which are (a) atoms in SAV chain, (b) atoms in whole protein, (c) atoms in other chains or molecules, (d) H -group, (e) V -group, (f)Z -group, (g) P -group, (h) F -groups, and (i)E -groups. The white and grey boxes represented the distribution of cancer-related and neutral SAVs. The boxes have the red frame if the significant difference is found at a 95% confidence interval by z-test between cancer-related and neutral SAVs. The label of selected descriptors by the genetic algorithm are bold in the x -axis. The symbol stars are noted as the cases D227Y of CD23.
FIGURE 5 The protein structure of the human skeletal calsequestrin. The structure of CASQ (PDB ID:3UOM) (Sanchez et al., 2012) is drawn in the cyan cartoon by PyMOL. All of the yellow bubbles are Ca2+ in CASQ. Three Ca2+ binding residues are highlighted with sticks in deep pink and the SAV, E194G is a cancer-related SAV.
FIGURE 6 The boxplot of the micro-environment descriptors in GLU altered to GLY sub-group. All micro-environment descriptors are divided in nine groups, which are (a) atoms in SAV chain, (b) atoms in whole protein, (c) atoms in other chains or molecules, (d) H -group, (e) V -group, (f) Z -group, (g) P -group, (h) F -groups, and (i) E -groups. The white and grey boxes represented the distribution of cancer-related and neutral SAVs. The label of selected descriptors by the genetic algorithm are bold in the x -axis. The symbol stars are noted as the cases E194G of CASQ.